HoloNet.plotting.feature_plot#
- HoloNet.plotting.feature_plot(feature_mat, adata, feature_names, plot_feature, size=1.4, fname=None, cutoff=None, scale=False, cell_alpha=0.7, cmap='Spectral_r', **kwargs)#
Plot one feature of each cell at the spatial position.
- Parameters
- feature_mat
Tensor|ndarrayUnion[Tensor,ndarray] A matrix containing features in each cell (CE centrality, or generated gene expression et al).
- adata
AnnData Annotated data matrix.
- feature_names
List[str] The names of all features.
- plot_feature
str The name of feature for plotting.
- size
float(default:1.4) The size of each spot, see sc.pl.spatial in Scanpy.
- fname
str|NoneOptional[str] (default:None) The output file name. If None, not save the figure. Note that not add path name, sc.pl.spatial will add ‘show’ before the file name.
- cutoff
str|NoneOptional[str] (default:None) The cutoff value (percentage) of the plotted feature.
- scale
bool(default:False) If True, will scale the feature value to make the maximum into 1.
- cell_alpha
float(default:0.7) The alpha value of each spot.
- cmap
Colormap|strUnion[Colormap,str] (default:'Spectral_r') The color map of feature value of each spot, defaultly as ‘Spectral_r’.
- kwargs
Other parameters in sc.pl.spatial
- feature_mat
- Return type